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- PDB-5d7e: Crystal structure of Taf14 YEATS domain in complex with H3K9ac -

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Basic information

Entry
Database: PDB / ID: 5d7e
TitleCrystal structure of Taf14 YEATS domain in complex with H3K9ac
Components
  • H3K9ac
  • Transcription initiation factor TFIID subunit 14
KeywordsNUCLEAR PROTEIN / acetylation histone YEATS reader
Function / homology
Function and homology information


NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Ino80 complex / mediator complex / transcription factor TFIIF complex / replication fork protection complex ...NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Ino80 complex / mediator complex / transcription factor TFIIF complex / replication fork protection complex / SWI/SNF complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / CENP-A containing nucleosome / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / transcription by RNA polymerase II / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA-templated transcription / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / YEATS domain / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / NET domain / Bromodomain extra-terminal - transcription regulation / Histone H3 signature 1. / Histone H3 signature 2. ...SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / YEATS domain / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / NET domain / Bromodomain extra-terminal - transcription regulation / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Transcription initiation factor TFIID subunit 14 / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAndrews, F.H. / Shanle, E.K. / Strahl, B.D. / Kutateladze, T.G.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110058 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100907 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K12-GM000678 United States
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)T32AA007464 United States
CitationJournal: Genes Dev. / Year: 2015
Title: Association of Taf14 with acetylated histone H3 directs gene transcription and the DNA damage response.
Authors: Shanle, E.K. / Andrews, F.H. / Meriesh, H. / McDaniel, S.L. / Dronamraju, R. / DiFiore, J.V. / Jha, D. / Wozniak, G.G. / Bridgers, J.B. / Kerschner, J.L. / Krajewski, K. / Martin, G.M. / ...Authors: Shanle, E.K. / Andrews, F.H. / Meriesh, H. / McDaniel, S.L. / Dronamraju, R. / DiFiore, J.V. / Jha, D. / Wozniak, G.G. / Bridgers, J.B. / Kerschner, J.L. / Krajewski, K. / Martin, G.M. / Morrison, A.J. / Kutateladze, T.G. / Strahl, B.D.
History
DepositionAug 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 14
C: H3K9ac
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4456
Polymers16,9312
Non-polymers5144
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-3 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.164, 113.164, 26.524
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Transcription initiation factor TFIID subunit 14 / Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling ...Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling complex subunit TAF14 / SWI/SNF complex 29 kDa subunit / SWI/SNF complex subunit TAF14 / TBP-associated factor 14 / TBP-associated factor 30 kDa / Transcription factor G 30 kDa subunit / Transcription initiation factor TFIIF 30 kDa subunit


Mass: 16026.331 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W / Production host: Escherichia coli (E. coli) / References: UniProt: P35189
#2: Protein/peptide H3K9ac


Mass: 904.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61830*PLUS
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M sodium citrate and 48% PEG600 (v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.98 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→56.52 Å / Num. obs: 15763 / % possible obs: 100 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 30.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
d*TREKdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→56 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2179 792 5.03 %
Rwork0.1847 --
obs0.1863 15750 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 33 67 1294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091273
X-RAY DIFFRACTIONf_angle_d1.221725
X-RAY DIFFRACTIONf_dihedral_angle_d13.501493
X-RAY DIFFRACTIONf_chiral_restr0.052191
X-RAY DIFFRACTIONf_plane_restr0.005223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9-2.01910.28481270.21192448
2.0191-2.1750.22911320.1842456
2.175-2.39380.25021260.192476
2.3938-2.74020.22471340.18992463
2.7402-3.45240.23271330.19232521
3.45240.19241400.17462594
Refinement TLS params.Method: refined / Origin x: 43.7059 Å / Origin y: 13.737 Å / Origin z: 1.3062 Å
111213212223313233
T0.238 Å20.0392 Å2-0.0064 Å2-0.1983 Å2-0.0402 Å2--0.2042 Å2
L2.0994 °2-2.4508 °20.5902 °2-5.9918 °2-0.7938 °2--0.9006 °2
S0.0866 Å °0.0594 Å °0.0525 Å °-0.0932 Å °-0.1194 Å °0.2075 Å °-0.1037 Å °-0.1338 Å °0.0464 Å °
Refinement TLS groupSelection details: all

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